Evolution of domain co-occurrences: some striking results

TL;DRAbstract

Investigation of the origin and evolution of regulatory mechanisms requires comparable estimates for the abundance and co-occurrence of functional protein domains of distantly related genomes. Currently available methods suffer for strong ascertainment biases, requiring methods for unbiased approaches to protein domain contents at genome-wide scales [1,4]. We will discuss domain distribution patterns between taxonomic groups providing insights into large-scale evolutionary trends. Since version 1.75, the SUPERFAMILY database provides functional information for protein domains using the gene ontology annotation terms [2,3]. To use the SUPERFAMILY database for comparison of GO annotation terms between species, one relies on existing, heavily biased gene annotation. To overcome this problem, we propose to perform gene prediction followed by the detection of protein domains via HMMs for SUPERFAMILY domains and subsequent analysis of the abundance and cooccurence of functionally related gro

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